Command
Line Version of ALSE

ALSE is written in C++, it can be compiled
with the GCC C++ compiler version 3.00 or above. You can
get the source code from the ALSE
webpage. The file is in the format ALSE_v????.tar.gz
where v???? is the version number.
Unix prompt is shown as "$". Un-tar the file
and compile the ALSE by doing:

$ tar zxvf ALSE_v???.tar.gz$ cd ALSE$ make clean$ make

If everything is smooth, you should get a executable
file "find_motif".

[OPTIONS] fields specify the parameters
used for running ALSE. They can be any of
the following, appeared in any order. When
a particular option is not set or not specified
in the command line, the default value is
used in ALSE.

The FASTA file format is used
to contain multiple DNA (protein) sequences.
It begins with a character > followed
by the name of the sequence; the sequence data
follow in the next line. More sequences are listed
in the file in the similar way.